In order to understand the expression profile of JAK (Lv-JAK) and STAT (Lv-STAT) genes in Litopenaeus vannamei during the infection of pathogenic bacteria, relative expressions of Lv-JAK and Lv-STAT genes were analyzed in this study. Relative expression profile of Lv-JAK and Lv-STAT in different tissues and during the infection of Bacillus thuringiensis were analyzed by semi-quantitative PCR and quantitative real-time PCR,respectively. The results showed that transcript of Lv-JAK and Lv-STAT was mainly detected in gill, intestine and heart. The relative expressions of Lv-JAK and Lv-STAT were significantly up-regulated in gill tissues at the middle and late stages of B. thuringiensis infection (24~72 h). In intestine, the relative expression of Lv-JAK was significantly up-regulated at 6 and 24 h, while that of Lv-STAT was significantly up-regulated at 24 and 72 h. These studies indicated that JAK and STAT participated in the innate immune response induced by B. thuringiensis in L. vannamei. Understanding the expression profile of JAK and STAT in response to B. thuringiensis infection will be helpful to study the function and regulatory mechanism of shrimp JAK/STAT signaling pathway in response to bacterial infection.